I don't know what I do, but now everything *is working fine.*
My last commands:

Reinstall Anaconda2

Trying to compile the RDKit

   - sudo tar xzvf RDKit_2016_03_1.tgz -C ~/anaconda2/
   - vim ~/.bashrc (update the variables with the new path of rdkit)
   - . ~/.bashrc
   - cd ~/anaconda2/rdkit
   - mkdir build
   - cd build
   - cmake -DRDK_BUILD_INCHI_SUPPORT=ON ..
   - make -j 4 (ERROR on 50%)
   - make install (ERROR on 24%)


sudo apt-get install python-rdkit librdkit1 rdkit-data
sudo apt-get update
conda install -c rdkit rdkit


--
Wandré Nunes de Pinho Veloso
Professor Assistente - Unifei - Campus Avançado de Itabira-MG
Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
Inteligência Computacional - UNIFEI
Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG

2017-09-14 18:28 GMT-03:00 Wandré <wandrevel...@gmail.com>:

> I really can't do this right...
> I am thinking in reinstall Ubuntu and try again. Now the RDKit doesn't
> works.
>
>
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
> Inteligência Computacional - UNIFEI
> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>
> 2017-09-14 15:07 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>
>> Hi Wandré,
>>
>> Sorry to see you in trouble again.
>>
>> If you see the massages then
>> # All requested packages already installed.
>> # packages in environment at /home/wandre/anaconda2:
>> #
>> rdkit                     2017.03.3           np111py27_1    rdkit
>>
>> so your rdkit should be at
>> /home/wandre/anaconda2/<some other folders>
>>
>> But it is trying to import from
>> /opt/rdkit-Release_2016_03_1/rdkit/
>>
>> So the path variable is still NOT correct. It is good to see that you
>> installed conda correctly and rdkit i think installed correctly.
>>
>> Therefore I suspect that you need to remove the previously path for rdkit
>> (you probably set those during installing from source).
>>
>> I forgot what linux command will do that for you. Have a great day!
>>
>> *** I will update the answer whenever I get the appropriate linux
>> command.
>>
>> - malitha
>>
>>
>>
>> On Thu, Sep 14, 2017 at 11:38 PM, Wandré <wandrevel...@gmail.com> wrote:
>>
>>> Thanks Malitha,
>>>
>>> When I install Anaconda I said yes to all questions.
>>> When I trying to reinstall the RDKit, this message appears:
>>>
>>> wandre@wandreLinux:~/anaconda2$ conda install -c rdkit rdkit
>>> Fetching package metadata ...........
>>> Solving package specifications: .
>>>
>>> # All requested packages already installed.
>>> # packages in environment at /home/wandre/anaconda2:
>>> #
>>> rdkit                     2017.03.3           np111py27_1    rdkit
>>>
>>> When I run "python", appears:
>>>
>>> Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016,
>>> 23:09:15)
>>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>> Anaconda is brought to you by Continuum Analytics.
>>> Please check out: http://continuum.io/thanks and https://anaconda.org
>>> >>> import rdkit
>>> >>> from rdkit import Chem
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18,
>>> in <module>
>>>     from rdkit import rdBase
>>> ImportError: cannot import name rdBase
>>>
>>>
>>> --
>>> Wandré Nunes de Pinho Veloso
>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>> UFMG
>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>> Inteligência Computacional - UNIFEI
>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>
>>> 2017-09-14 9:17 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>>>
>>>> Hi Wandré,
>>>>
>>>> Good day! It's malitha.
>>>>
>>>> Considering your first question I would say, the path variable NOT set
>>>> correctly. To avoid having gymnastic with linux system you may consider the
>>>> following steps:
>>>>
>>>>    1. Install miniconda or andcona from https://conda.io/miniconda.html
>>>>    and command yes (y) when it says to add path variable to python shipped
>>>>    with conda. I mean python within conda would be your default python. 
>>>> After
>>>>    installing it, when you run the command <<<<<python>>>>>> from shell you
>>>>    will see something like <<<Continuum Analytics>>> at the screen
>>>>    2. Install rdkit from https://anaconda.org/rdkit/rdkit on top of
>>>>    conda
>>>>
>>>>
>>>> For question regarding energy minimization, you may find the following
>>>> link helpful.
>>>> https://sourceforge.net/p/rdkit/mailman/message/28298074/
>>>>
>>>> I hope, it helps!
>>>>
>>>> - malitha
>>>>
>>>> On Thu, Sep 14, 2017 at 4:22 PM, Wandré <wandrevel...@gmail.com> wrote:
>>>>
>>>>> So,
>>>>> 1) I run all the commands in tutorial of installation of RDKit in
>>>>> Conda (https://github.com/rdkit/conda-rdkit), but, when I run python
>>>>> and try to import Chem ("from rdkit import Chem") appears an error 
>>>>> message:
>>>>> Traceback (most recent call last):
>>>>>   File "<stdin>", line 1, in <module>
>>>>>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line
>>>>> 18, in <module>
>>>>>     from rdkit import rdBase
>>>>> ImportError: cannot import name rdBase
>>>>>
>>>>> 2) Thanks for all the references
>>>>>
>>>>> 3) Which function generate this "energy minimized molecule"?
>>>>>
>>>>> --
>>>>> Wandré Nunes de Pinho Veloso
>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>>>> UFMG
>>>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>>>> Inteligência Computacional - UNIFEI
>>>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>>>
>>>>> 2017-09-13 17:32 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>>>>>
>>>>>> Hi Wandré,
>>>>>>
>>>>>> 1) apt-get installs rdkit 2013 (link below). So, please install it
>>>>>> through conda (as Markus suggested)
>>>>>> https://packages.ubuntu.com/trusty/python/python-rdkit
>>>>>>
>>>>>> 2) I am not familiar with the case of wrong SMILE generation. But the
>>>>>> link below says something more that I think you need to know.
>>>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495655/
>>>>>>
>>>>>> 3) As you are trying to store data, it would be great to consider
>>>>>> whether you are storing energy minimized molecule or not. (my opinion).
>>>>>> Surface area related descriptors will yield different result and bond
>>>>>> connectivity related descriptor will yield same result in both cases.
>>>>>>
>>>>>> 4) Sharing my personal experience, during my undergraduate school
>>>>>> part of my final year project was stressed up with conceptual questions. 
>>>>>> I
>>>>>> failed to utilize the  blessing of advanced development due to the lack 
>>>>>> of
>>>>>> time. The later experience was not so good.
>>>>>>
>>>>>> Please keep in mind that we can generate a non redundant database
>>>>>> with few molecules but for millions of molecules it should be quite 
>>>>>> though
>>>>>> task. Have a great day!
>>>>>>
>>>>>> - malitha
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Sep 14, 2017 at 2:05 AM, Markus Sitzmann <
>>>>>> markus.sitzm...@gmail.com> wrote:
>>>>>>
>>>>>>> PS. The conda version has InChI support
>>>>>>>
>>>>>>> On Wed, Sep 13, 2017 at 10:04 PM, Markus Sitzmann <
>>>>>>> markus.sitzm...@gmail.com> wrote:
>>>>>>>
>>>>>>>> Strong recommendation: use the conda version:
>>>>>>>>
>>>>>>>> http://www.rdkit.org/docs/Install.html
>>>>>>>>
>>>>>>>> On Wed, Sep 13, 2017 at 9:58 PM, Wandré <wandrevel...@gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I just run sudo apt-get install python-rdkit librdkit1
>>>>>>>>> rdkit-data 😁
>>>>>>>>> I'm trying to solve this with this link: http://www.blopig.com/bl
>>>>>>>>> og/2013/02/how-to-install-rdkit-on-ubuntu-12-04/
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Wandré Nunes de Pinho Veloso
>>>>>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>>>>>> Doutorando em Bioinformática - Universidade Federal de Minas
>>>>>>>>> Gerais - UFMG
>>>>>>>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>>>>>>>> Inteligência Computacional - UNIFEI
>>>>>>>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>>>>>>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>>>>>>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>>>>>>>
>>>>>>>>> 2017-09-13 16:55 GMT-03:00 Markus Sitzmann <
>>>>>>>>> markus.sitzm...@gmail.com>:
>>>>>>>>>
>>>>>>>>>> How did you install rdkit so far? And where? Is it the
>>>>>>>>>> conda/anaconda version?
>>>>>>>>>>
>>>>>>>>>> On Wed, Sep 13, 2017 at 9:39 PM, Wandré <wandrevel...@gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> How to install RDKit with InChI?
>>>>>>>>>>> When I run Chem.inchi.INCHI_AVAILABLE, the result is False
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Wandré Nunes de Pinho Veloso
>>>>>>>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>>>>>>>> Doutorando em Bioinformática - Universidade Federal de Minas
>>>>>>>>>>> Gerais - UFMG
>>>>>>>>>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>>>>>>>>>> Inteligência Computacional - UNIFEI
>>>>>>>>>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>>>>>>>>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>>>>>>>>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>>>>>>>>>
>>>>>>>>>>> 2017-09-13 16:30 GMT-03:00 Wandré <wandrevel...@gmail.com>:
>>>>>>>>>>>
>>>>>>>>>>>> Thanks Malitha.
>>>>>>>>>>>> I choose this descriptors because I will store this on my
>>>>>>>>>>>> database, so, will be fast compare one molecule before insert them 
>>>>>>>>>>>> in
>>>>>>>>>>>> database.
>>>>>>>>>>>> My worry now is if the RDKit will generate different SMILES or
>>>>>>>>>>>> InChI in same SDF molecule or equals in different molecules 
>>>>>>>>>>>> (molecules from
>>>>>>>>>>>> RCSB PDB, PubChem, ChemBL, for example).
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Wandré Nunes de Pinho Veloso
>>>>>>>>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>>>>>>>>> Doutorando em Bioinformática - Universidade Federal de Minas
>>>>>>>>>>>> Gerais - UFMG
>>>>>>>>>>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>>>>>>>>>>> Inteligência Computacional - UNIFEI
>>>>>>>>>>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>>>>>>>>>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>>>>>>>>>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>>>>>>>>>>
>>>>>>>>>>>> 2017-09-13 16:22 GMT-03:00 Malitha Kabir <
>>>>>>>>>>>> malitha12...@gmail.com>:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Wandré,
>>>>>>>>>>>>>
>>>>>>>>>>>>> It seems you already did intense research on it. Kindly accept
>>>>>>>>>>>>> my comments as an addition to your idea (not the answer you 
>>>>>>>>>>>>> trying to find
>>>>>>>>>>>>> out). In my idea, categorizing molecules using it's descriptor 
>>>>>>>>>>>>> should
>>>>>>>>>>>>> reduce computation time. RDKit currently offer calculation of 
>>>>>>>>>>>>> about 200
>>>>>>>>>>>>> descriptors! So, a careful look up at those makes a lot of sense 
>>>>>>>>>>>>> to me.
>>>>>>>>>>>>> Conceptually, descriptor matching should follow a sequence (I 
>>>>>>>>>>>>> don't know
>>>>>>>>>>>>> what sequence would be ideal) - for example MolWt should match 
>>>>>>>>>>>>> first (H
>>>>>>>>>>>>> contribution and ions should be taken into consideration here) 
>>>>>>>>>>>>> and then
>>>>>>>>>>>>> subsequent matching of other descriptors (might be different 
>>>>>>>>>>>>> while writing
>>>>>>>>>>>>> programs). There are a few reading materials on molecular 
>>>>>>>>>>>>> fingerprint and
>>>>>>>>>>>>> database schema. You may have a look at those.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The links are from Daylight. I am neither involved with the
>>>>>>>>>>>>> company nor their product.
>>>>>>>>>>>>> http://www.daylight.com/dayhtml/doc/theory/theory.finger.html
>>>>>>>>>>>>> http://www.daylight.com/dayhtml/doc/theory/theory.thor.html
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>> - malitha
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Sep 14, 2017 at 12:43 AM, Wandré <
>>>>>>>>>>>>> wandrevel...@gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks for all the answers.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Reading all answers, I think in something different... If the
>>>>>>>>>>>>>> SMILES (Chem.MolToSmiles(mol,isomericSmiles=True)) and Inchi
>>>>>>>>>>>>>> (Chem.MolToInchi(mol)) can generate the same value in different 
>>>>>>>>>>>>>> molecules,
>>>>>>>>>>>>>> I will generate others descriptors (NumHDonors, NumHAcceptors, Ri
>>>>>>>>>>>>>> ngCount, GetNumAtoms, TPSA, pyLabuteASA, MolWt, 
>>>>>>>>>>>>>> CalcNumRotatableBonds
>>>>>>>>>>>>>> and MolLogP) to compare all the molecules that SMILES and Inchi 
>>>>>>>>>>>>>> are the
>>>>>>>>>>>>>> same.
>>>>>>>>>>>>>> If all this data are the same, I will generate the
>>>>>>>>>>>>>> fingerprint (Atompair for exemple) and use Tanimoto coefficient 
>>>>>>>>>>>>>> and, if
>>>>>>>>>>>>>> this value, when I compare two molecules, is 1, this molecules 
>>>>>>>>>>>>>> are the same.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Where is my mistake (I think that is, one or more, mistakes)?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Wandré Nunes de Pinho Veloso
>>>>>>>>>>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>>>>>>>>>>> Doutorando em Bioinformática - Universidade Federal de Minas
>>>>>>>>>>>>>> Gerais - UFMG
>>>>>>>>>>>>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação
>>>>>>>>>>>>>> e Inteligência Computacional - UNIFEI
>>>>>>>>>>>>>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>>>>>>>>>>>>>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>>>>>>>>>>>>>> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2017-09-13 14:19 GMT-03:00 Dimitri Maziuk <
>>>>>>>>>>>>>> dmaz...@bmrb.wisc.edu>:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 09/13/2017 11:46 AM, Markus Sitzmann wrote:
>>>>>>>>>>>>>>> > The case that you have 3D information available for a
>>>>>>>>>>>>>>> molecule dataset is rare, if you want it trustworthy it gets 
>>>>>>>>>>>>>>> even worse
>>>>>>>>>>>>>>> than that. And what is the point then to generate the 
>>>>>>>>>>>>>>> configuration of a
>>>>>>>>>>>>>>> molecule first if you can not trust that either?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Veering further off topic, do you even care in the first
>>>>>>>>>>>>>>> place? E.g. if
>>>>>>>>>>>>>>> your molecule always exists as a mixture of isomers, except
>>>>>>>>>>>>>>> in some
>>>>>>>>>>>>>>> megabuck-per-microgram painstakingly created reference
>>>>>>>>>>>>>>> samples, a
>>>>>>>>>>>>>>> 3D-based system will represent it as two distinct molecules.
>>>>>>>>>>>>>>> Whereas you
>>>>>>>>>>>>>>> want it represented as one.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Last I looked PDB Ligand Expo had two different benzenes.
>>>>>>>>>>>>>>> Their software
>>>>>>>>>>>>>>> doesn't (didn't?) do the circle version so they don't have
>>>>>>>>>>>>>>> the third one.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> Dimitri Maziuk
>>>>>>>>>>>>>>> Programmer/sysadmin
>>>>>>>>>>>>>>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>>>> ------------------
>>>>>>>>>>>>>>> Check out the vibrant tech community on one of the world's
>>>>>>>>>>>>>>> most
>>>>>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Rdkit-discuss mailing list
>>>>>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>>> ------------------
>>>>>>>>>>>>>> Check out the vibrant tech community on one of the world's
>>>>>>>>>>>>>> most
>>>>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Rdkit-discuss mailing list
>>>>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>> ------------------
>>>>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Rdkit-discuss mailing list
>>>>>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------
>>>>>>> ------------------
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>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>> _______________________________________________
>>>>>>> Rdkit-discuss mailing list
>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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